tests/testthat/test-methodsMeanExpression.R

In jhsiao999/ashbun: Methods and evaluation tools for single cell RNA-seq count data

test_that("methods return pvalues not NAs", {
  ipsc_eset <- get(load(system.file("testdata", "HumanTungiPSC.rda", package = "ashbun")))
  count_matrix <- exprs(ipsc_eset)[sample(nrow(exprs(ipsc_eset)), 500), ]
  condition <- pData(ipsc_eset)$replicate
  
  methods <- c("methodWrapper.DESeq2",
               "methodWrapper.edgeR",
               "methodWrapper.limmaVoom",
               "methodWrapper.bpsc",
               "methodWrapper.mast",
               "methodWrapper.rots")
#"methodWrapper.scde", 

  for (index in 1:length(methods)) {
    output <- do.call(methods[index], list(count_matrix, condition))
    source("common-methodsMeanExpression.R", local = TRUE)
  }

})